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Xiao C, Xiao D, Sun M, Wang K. Bacteria, Fungi, and Protists Exhibit Distinct Responses to Managed Vegetation Restoration in the Karst Region. Microorganisms 2024; 12:1074. [PMID: 38930456 PMCID: PMC11205577 DOI: 10.3390/microorganisms12061074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Bacteria, fungi, and protists occupy a pivotal position in maintaining soil ecology. Despite limited knowledge on their responses to managed vegetation restoration strategies in karst regions, we aimed to study the essential microbial communities involved in the process of vegetation restoration. We compared microbial characteristics in four land use types: planted forests (PF), forage grass (FG), a mixture of plantation forest and forage grass (FF), and cropland (CR) as a reference. Our findings revealed that the richness of bacteria and protists was higher in FF compared to PF, while fungal richness was lower in both PF and FF than in CR. Additionally, the bacterial Shannon index in FF was higher than that in CR and PF, while the fungal and protist Shannon indices were similar across all four land use types. Significant differences were observed in the compositions of bacterial, fungal, and protist communities between FF and the other three land use types, whereas bacterial, fungal, and protist communities were relatively similar in PF and FG. In FF, the relative abundance of bacterial taxa Acidobacteria, Firmicutes, and Gemmatimonadetes was significantly higher than in PF and CR. Fungal communities were dominated by Ascomycota and Basidiomycota, with the relative abundance of Ascomycota significantly higher in FF compared to other land use types. Regarding protistan taxa, the relative abundance of Chlorophyta was higher in FF compared to CR, PF, and FG, while the relative abundance of Apicomplexa was higher in CR compared to FF. Importantly, ammonium nitrogen, total phosphorus, and microbial biomass nitrogen were identified as key soil properties predicting changes in the diversity of bacteria, fungi, and protists. Our results suggest that the microbial community under FF exhibits greater sensitivity to vegetation restoration compared to PF and FG. This sensitivity may stem from differences in soil properties, the formation of biological crusts and root systems, and management activities, resulting in variations in bacterial, fungal, and protist diversity and taxa in PF. As a result, employing a combination restoration strategy involving plantation forest and forage grass proves to be an effective approach to enhance the microbial community and thereby improve ecosystem functionality in ecologically fragile areas.
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Affiliation(s)
- Can Xiao
- College of Environment and Ecology, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China;
- Huanjiang Agriculture Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
| | - Dan Xiao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China;
- Huanjiang Agriculture Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
| | - Mingming Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China;
- Huanjiang Agriculture Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Kelin Wang
- Huanjiang Agriculture Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
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Wang YF, Chen P, Wang FH, Han WX, Qiao M, Dong WX, Hu CS, Zhu D, Chu HY, Zhu YG. The ecological clusters of soil organisms drive the ecosystem multifunctionality under long-term fertilization. ENVIRONMENT INTERNATIONAL 2022; 161:107133. [PMID: 35149447 DOI: 10.1016/j.envint.2022.107133] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Long-term fertilization is known to impact the biodiversity and community structures of soil organisms, which are responsible for multiple soil ecosystem functions (multifunctionality). However the relationship between the alterations of soil organisms and ecosystem multifunctionality remains unclear, especially in the case of long-term fertilization. To explore the contribution of soil organismal biodiversity and community structures to ecosystem multifunctionality, we took soil samples from a nearly 25-year field fertilization experiment. Organic matter significantly improved the soil ecosystem multifunctionality. Ecosystem multifunctionality was found to be closely linked to the biodiversity and communities of soil organisms within the major ecological clustering of soil organisms (Module 1) according to the trophic co-occurrence network, rather than the entire community of soil organisms. This indicated that ecological clusters of soil organisms within the network were critical in maintaining soil ecosystem multifunctionality. The application of organic fertilization could enrich specialized soil organisms and increase interactions of soil organisms in the ecological cluster. As a result, our findings emphasize the role of ecological clusters in the soil organismal co-occurrence network in controlling soil multifunctionality after long-term fertilization, presenting a novel perspective on the link between soil biodiversity and ecosystem multifunctionality.
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Affiliation(s)
- Yi-Fei Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Peng Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Feng-Hua Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resource and Environment Sciences, Hebei Key Laboratory of Environmental Change and Ecological Construction, Hebei Normal University, Shijiazhuang 050024, China
| | - Wan-Xue Han
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wen-Xu Dong
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Chun-Sheng Hu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Hai-Yan Chu
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
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3
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Shi Y, Li Y, Yang T, Chu H. Threshold effects of soil pH on microbial co-occurrence structure in acidic and alkaline arable lands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149592. [PMID: 34426307 DOI: 10.1016/j.scitotenv.2021.149592] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/20/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Soil pH plays a pivotal role in shaping microbial diversity and community composition in terrestrial ecosystems. Soil microbes clearly do not exist independently and instead form complex interaction networks, but little is known about the effect of soil pH upon those microbial co-occurrence networks. In this study, 62 alkaline and 61 acidic soil samples were collected from the North China Plain to investigate the effect of soil pH on microbial co-occurrence structure. Most bacterial and fungal OTUs in acidic soils were maximally abundant at soil pH of ~5.5, while in alkaline soils the corresponding OTU abundance attainted its maximum at pH ~8.3. Unlike those OTU abundance distributions, the relationship between soil pH and the number of links between OTUs in the co-occurrence network was best fitted by convex curves, with the pH thresholds found at 5.39 for bacteria and 5.60 for fungi in acidic soils. In alkaline soils, a dip in the relationship (only for fungi) between soil pH and the links was also observed, with a pH threshold at 8.04 for bacteria and 8.28 for fungi. From the co-occurrence analysis we identified 37 core bacterial species (mainly in Actinobacteria and Proteobacteria) and 24 core fungal species (mainly in Ascomycota). Together, this study revealed the threshold effects of soil pH upon microbial co-occurrence structure and identified the core microbial species in the North China Plain. These findings provide baseline information in mediating soil microbial co-occurrence structure by adjusting soil pH and core species in croplands.
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Affiliation(s)
- Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China; A State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuntao Li
- A State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Teng Yang
- A State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Chu
- A State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China.
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Lütkenhaus R, Breuer J, Nowrousian M. Functional characterization of the developmental genes asm2, asm3, and spt3 required for fruiting body formation in the filamentous ascomycete Sordaria macrospora. Genetics 2021; 219:iyab103. [PMID: 34849873 PMCID: PMC8633134 DOI: 10.1093/genetics/iyab103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/30/2021] [Indexed: 01/10/2023] Open
Abstract
The formation of fruiting bodies is one of the most complex developmental processes in filamentous ascomycetes. It requires the development of sexual structures that give rise to meiosporangia (asci) and meiotic spores (ascospores) as well as surrounding structures for protection and dispersal of the spores. Previous studies have shown that these developmental processes are accompanied by significant changes of the transcriptome, and comparative transcriptomics of different fungi as well as the analysis of transcriptome changes in developmental mutants have aided in the identification of differentially regulated genes that are themselves involved in regulating fruiting body development. In previous analyses, we used transcriptomics to identify the genes asm2 and spt3, which result in developmental phenotypes when deleted in Sordaria macrospora. In this study, we identified another gene, asm3, required for fruiting body formation, and performed transcriptomics analyses of Δasm2, Δasm3, and Δspt3. Deletion of spt3, which encodes a subunit of the SAGA complex, results in a block at an early stage of development and drastic changes in the transcriptome. Deletion mutants of asm2 and asm3 are able to form fruiting bodies, but have defects in ascospore maturation. Transcriptomics analysis of fruiting bodies revealed a large overlap in differentially regulated genes in Δasm2 and Δasm3 compared to the wild type. Analysis of nuclear distribution during ascus development showed that both mutants undergo meiosis and postmeiotic divisions, suggesting that the transcriptomic and morphological changes might be related to defects in the morphogenesis of structural features of the developing asci and ascospores.
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Affiliation(s)
- Ramona Lütkenhaus
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Jan Breuer
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
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Arid Ecosystem Vegetation Canopy-Gap Dichotomy: Influence on Soil Microbial Composition and Nutrient Cycling Functional Potential. Appl Environ Microbiol 2021; 87:AEM.02780-20. [PMID: 33310716 PMCID: PMC8090872 DOI: 10.1128/aem.02780-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Increasing temperatures and drought in desert ecosystems are predicted to cause decreased vegetation density combined with barren ground expansion. It remains unclear how nutrient availability, microbial diversity, and the associated functional capacity vary between vegetated-canopy and gap soils. The specific aim of this study was to characterize canopy vs gap microsite effect on soil microbial diversity, the capacity of gap soils to serve as a canopy-soil microbial reservoir, nitrogen (N)-mineralization genetic potential (ureC gene abundance) and urease enzyme activity, and microbial-nutrient pool associations in four arid-hyperarid geolocations of the western Sonoran Desert, Arizona (USA). Microsite combined with geolocation explained 57% and 45.8% of the observed variation in bacterial/archaeal and fungal community composition, respectively. A core microbiome of amplicon sequence variants was shared between the canopy and gap soil communities; however, canopy-soils included abundant taxa that were not present in associated gap communities, thereby suggesting that these taxa cannot be sourced from the associated gap soils. Linear mixed-effects models showed that canopy-soils have significantly higher microbial richness, nutrient content, and organic N-mineralization genetic and functional capacity. Furthermore, ureC gene abundance was detected in all samples suggesting that ureC is a relevant indicator of N-mineralization in deserts. Additionally, novel phylogenetic associations were observed for ureC with the majority belonging to Actinobacteria and uncharacterized bacteria. Thus, key N-mineralization functional capacity is associated with a dominant desert phylum. Overall, these results suggest that lower microbial diversity and functional capacity in gap soils may impact ecosystem sustainability as aridity drives open-space expansion in deserts.
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The Glyoxysomal Protease LON2 Is Involved in Fruiting-Body Development, Ascosporogenesis and Stress Resistance in Sordaria macrospora. J Fungi (Basel) 2021; 7:jof7020082. [PMID: 33530609 PMCID: PMC7911957 DOI: 10.3390/jof7020082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 01/05/2023] Open
Abstract
Microbodies, including peroxisomes, glyoxysomes and Woronin bodies, are ubiquitous dynamic organelles that play important roles in fungal development. The ATP-dependent chaperone and protease family Lon that maintain protein quality control within the organelle significantly regulate the functionality of microbodies. The filamentous ascomycete Sordaria macrospora is a model organism for studying fruiting-body development. The genome of S. macrospora encodes one Lon protease with the C-terminal peroxisomal targeting signal (PTS1) serine-arginine-leucine (SRL) for import into microbodies. Here, we investigated the function of the protease SmLON2 in sexual development and during growth under stress conditions. Localization studies revealed a predominant localization of SmLON2 in glyoxysomes. This localization depends on PTS1, since a variant without the C-terminal SRL motif was localized in the cytoplasm. A ΔSmlon2 mutant displayed a massive production of aerial hyphae, and produced a reduced number of fruiting bodies and ascospores. In addition, the growth of the ΔSmlon2 mutant was completely blocked under mild oxidative stress conditions. Most of the defects could be complemented with both variants of SmLON2, with and without PTS1, suggesting a dual function of SmLON2, not only in microbody, but also in cytosolic protein quality control.
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Wu J, Choi J, Asiegbu FO, Lee YH. Comparative Genomics Platform and Phylogenetic Analysis of Fungal Laccases and Multi-Copper Oxidases. MYCOBIOLOGY 2020; 48:373-382. [PMID: 33177916 PMCID: PMC7594830 DOI: 10.1080/12298093.2020.1816151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
Laccases (EC 1.10.3.2), a group of multi-copper oxidases (MCOs), play multiple biological functions and widely exist in many species. Fungal laccases have been extensively studied for their industrial applications, however, there was no database specially focused on fungal laccases. To provide a comparative genomics platform for fungal laccases, we have developed a comparative genomics platform for laccases and MCOs (http://laccase.riceblast.snu.ac.kr/). Based on protein domain profiles of characterized sequences, 3,571 laccases were predicted from 690 genomes including 253 fungi. The number of putative laccases and their properties exhibited dynamic distribution across the taxonomy. A total of 505 laccases from 68 genomes were selected and subjected to phylogenetic analysis. As a result, four clades comprised of nine subclades were phylogenetically grouped by their putative functions and analyzed at the sequence level. Our work would provide a workbench for putative laccases mainly focused on the fungal kingdom as well as a new perspective in the identification and classification of putative laccases and MCOs.
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Affiliation(s)
- Jiayao Wu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Jaeyoung Choi
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
| | - Fred O. Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Plant Immunity Research Center, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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Lourenço KS, Suleiman AKA, Pijl A, Cantarella H, Kuramae EE. Dynamics and resilience of soil mycobiome under multiple organic and inorganic pulse disturbances. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139173. [PMID: 32454291 DOI: 10.1016/j.scitotenv.2020.139173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Disturbances in soil can cause short-term soil changes, consequently changes in microbial community what may result in long-lasting ecological effects. Here, we evaluate how multiple pulse disturbances effect the dynamics and resilience of fungal community, and the co-occurrence of fungal and bacterial communities in a 389 days field experiment. We used soil under sugarcane cultivation as soil ecosystem model, and organic residue (vinasse - by-product of sugarcane ethanol production) combined or not with inorganic (organic residue applied 30 days before or together with mineral N fertilizer) amendments as disturbances. Application of organic residue alone as a single disturbance or 30 days prior to a second disturbance with mineral N resulted in similar changes in the fungal community. The simultaneous application of organic and mineral N as a single pulse disturbance had the greatest impact on the fungal community. Organic amendment increased the abundance of saprotrophs, fungal species capable of denitrification, and fungi described to have copiotrophic and oligotrophic lifestyles. Furthermore, the changes in the fungal community were not correlated with the changes in the bacterial community. The fungal community was neither resistant nor resilient to organic and inorganic disturbances over the one-year sampling period. Our findings provide insights on the immediate and delayed responses of the fungal community over one year to disturbance by organic and inorganic amendments.
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Affiliation(s)
- Késia Silva Lourenço
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, SP, Brazil
| | - Afnan Khalil Ahmad Suleiman
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; KWR Watercycle Research Institute, Groningenhaven 7, 3433, PE, Nieuwegein, The Netherlands
| | - Agata Pijl
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, SP, Brazil
| | - Eiko Eurya Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
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Multicopper Oxidases in Saccharomyces cerevisiae and Human Pathogenic Fungi. J Fungi (Basel) 2020; 6:jof6020056. [PMID: 32349384 PMCID: PMC7345259 DOI: 10.3390/jof6020056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/20/2020] [Accepted: 04/25/2020] [Indexed: 12/11/2022] Open
Abstract
Multicopper oxidases (MCOs) are produced by microscopic and macroscopic fungal species and are involved in various physiological processes such as morphogenesis, lignin degradation, and defense mechanisms to stress inducing environmental conditions as well as fungal virulence. This review will summarize our current understanding regarding the functions of MCOs present in Saccharomyces cerevisiae and in different human fungal pathogens. Of the two main MCO groups, the first group of MCOs is involved in iron homoeostasis and the second includes laccases. This review will also discuss their role in the pathogenesis of human fungal pathogens.
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Xie N, Ruprich-Robert G, Silar P, Herbert E, Ferrari R, Chapeland-Leclerc F. Characterization of three multicopper oxidases in the filamentous fungus Podospora anserina: A new role of an ABR1-like protein in fungal development? Fungal Genet Biol 2018; 116:1-13. [PMID: 29654834 DOI: 10.1016/j.fgb.2018.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 11/16/2022]
Abstract
The Podospora anserina genome contains a large family of 15 multicopper oxidases (MCOs), including three genes encoding a FET3-like protein, an ABR1-like protein and an ascorbate oxidase (AO)-like protein. FET3, ABR1 and AO1 are involved in global laccase-like activity since deletion of the relevant genes led to a decrease of activity when laccase substrate (ABTS) was used as substrate. However, contrary to the P. anserina MCO proteins previously characterized, none of these three MCOs seemed to be involved in lignocellulose degradation and in resistance to phenolic compounds and oxidative stress. We showed that the bulk of ferroxidase activity was clearly due to ABR1, and only in minor part to FET3, although ABR1 does not contain all the residues typical of FET3 proteins. Moreover, we showed that ABR1, related to the Aspergillus fumigatus ABR1 protein, was clearly and specifically involved in pigmentation of ascospores. Surprisingly, phenotypes were more severe in mutants lacking both abr1 and ao1. Deletion of the ao1 gene led to an almost total loss of AO activity. No direct involvement of AO1 in fungal developmental process in P. anserina was evidenced, except in a abr1Δ background. Overall, unlike other previously characterized MCOs, we thus evidence a clear involvement of ABR1 protein in fungal development.
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Affiliation(s)
- Ning Xie
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), UMR 8236, 75205 Paris, France
| | - Gwenaël Ruprich-Robert
- Univ Paris Descartes, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), UMR 8236, 75205 Paris, France
| | - Philippe Silar
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), UMR 8236, 75205 Paris, France
| | - Eric Herbert
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), UMR 8236, 75205 Paris, France
| | - Roselyne Ferrari
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), UMR 8236, 75205 Paris, France
| | - Florence Chapeland-Leclerc
- Univ Paris Descartes, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), UMR 8236, 75205 Paris, France.
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11
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She W, Bai Y, Zhang Y, Qin S, Feng W, Sun Y, Zheng J, Wu B. Resource Availability Drives Responses of Soil Microbial Communities to Short-term Precipitation and Nitrogen Addition in a Desert Shrubland. Front Microbiol 2018; 9:186. [PMID: 29479346 PMCID: PMC5811472 DOI: 10.3389/fmicb.2018.00186] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/26/2018] [Indexed: 11/13/2022] Open
Abstract
Desert microbes are expected to be substantially sensitive to global environmental changes, such as precipitation changes and elevated nitrogen deposition. However, the effects of precipitation changes and nitrogen enrichment on their diversity and community composition remain poorly understood. We conducted a field experiment over 2 years with multi-level precipitation and nitrogen addition in a desert shrubland of northern China, to examine the responses of soil bacteria and fungi in terms of diversity and community composition and to explore the roles of plant and soil factors in structuring microbial communities. Water addition significantly increased soil bacterial diversity and altered the community composition by increasing the relative abundances of stress-tolerant (dormant) taxa (e.g., Acidobacteria and Planctomycetes); however, nitrogen addition had no substantial effects. Increased precipitation and nitrogen did not impact soil fungal diversity, but significantly shifted the fungal community composition. Specifically, water addition reduced the relative abundances of drought-tolerant taxa (e.g., the orders Pezizales, Verrucariales, and Agaricales), whereas nitrogen enrichment decreased those of oligotrophic taxa (e.g., the orders Agaricales and Sordariales). Shifts in microbial community composition under water and nitrogen addition occurred primarily through changing resource availability rather than plant community. Our results suggest that water and nitrogen addition affected desert microbes in different ways, with watering shifting stress-tolerant traits and fertilization altering copiotrophic/oligotrophic traits of the microbial communities. These findings highlight the importance of resource availability in driving the desert microbial responses to short-term environmental changes.
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Affiliation(s)
- Weiwei She
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, China
| | - Yuxuan Bai
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, China
| | - Yuqing Zhang
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, China.,Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, China
| | - Shugao Qin
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, China.,Engineering Research Center of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing, China
| | - Wei Feng
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, China.,Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, China
| | - Yanfei Sun
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, China
| | - Jing Zheng
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, China
| | - Bin Wu
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, China.,Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, China
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Cai L, Krafft T, Chen TB, Lv WZ, Gao D, Zhang HY. New insights into biodrying mechanism associated with tryptophan and tyrosine degradations during sewage sludge biodrying. BIORESOURCE TECHNOLOGY 2017; 244:132-141. [PMID: 28779664 DOI: 10.1016/j.biortech.2017.07.118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/17/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
Abstract
Sewage sludge biodrying is a treatment that uses bio-heat generated from organic degradation to remove water from sewage sludge. Dewatering is still limited during biodrying, due to the presence of extracellular polymeric substances (EPS) in sludge. To study the biodrying mechanism associated with EPS compositions tryptophan and tyrosine degradations, this study investigated the microbial function in sludge biodrying material. This study conducted a taxonomic analysis of biodrying material; determined the most abundant genetic functions; analyzed the functional microorganisms involved in the degradations of tryptophan and tyrosine; and summarized the metabolic pathways. The results indicated efficient degradations of tryptophan and tyrosine were observed during the initial thermophilic phase; functional microorganisms were mainly from the phyla Firmicutes, Actinobacteria, and Proteobacteria, enriched with genes involved in amino acid transport and metabolism. These findings highlight the potentially important microorganisms and typical pathways that may help improve dewaterability during biodegradation.
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Affiliation(s)
- Lu Cai
- Faculty of Architectural, Civil Engineering and Environment, Ningbo University, Ningbo 315211, China; Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht 6200 MD, The Netherlands.
| | - Thomas Krafft
- Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht 6200 MD, The Netherlands
| | - Tong-Bin Chen
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Zhou Lv
- Faculty of Architectural, Civil Engineering and Environment, Ningbo University, Ningbo 315211, China
| | - Ding Gao
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Han-Yan Zhang
- Faculty of Architectural, Civil Engineering and Environment, Ningbo University, Ningbo 315211, China
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Nelsen MP, DiMichele WA, Peters SE, Boyce CK. Delayed fungal evolution did not cause the Paleozoic peak in coal production. Proc Natl Acad Sci U S A 2016; 113:2442-7. [PMID: 26787881 PMCID: PMC4780611 DOI: 10.1073/pnas.1517943113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Organic carbon burial plays a critical role in Earth systems, influencing atmospheric O2 and CO2 concentrations and, thereby, climate. The Carboniferous Period of the Paleozoic is so named for massive, widespread coal deposits. A widely accepted explanation for this peak in coal production is a temporal lag between the evolution of abundant lignin production in woody plants and the subsequent evolution of lignin-degrading Agaricomycetes fungi, resulting in a period when vast amounts of lignin-rich plant material accumulated. Here, we reject this evolutionary lag hypothesis, based on assessment of phylogenomic, geochemical, paleontological, and stratigraphic evidence. Lignin-degrading Agaricomycetes may have been present before the Carboniferous, and lignin degradation was likely never restricted to them and their class II peroxidases, because lignin modification is known to occur via other enzymatic mechanisms in other fungal and bacterial lineages. Furthermore, a large proportion of Carboniferous coal horizons are dominated by unlignified lycopsid periderm with equivalent coal accumulation rates continuing through several transitions between floral dominance by lignin-poor lycopsids and lignin-rich tree ferns and seed plants. Thus, biochemical composition had little relevance to coal accumulation. Throughout the fossil record, evidence of decay is pervasive in all organic matter exposed subaerially during deposition, and high coal accumulation rates have continued to the present wherever environmental conditions permit. Rather than a consequence of a temporal decoupling of evolutionary innovations between fungi and plants, Paleozoic coal abundance was likely the result of a unique combination of everwet tropical conditions and extensive depositional systems during the assembly of Pangea.
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Affiliation(s)
| | - William A DiMichele
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Shanan E Peters
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI 53706
| | - C Kevin Boyce
- Geological Sciences, Stanford University, Stanford, CA 94305;
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Nagy LG, Riley R, Tritt A, Adam C, Daum C, Floudas D, Sun H, Yadav JS, Pangilinan J, Larsson KH, Matsuura K, Barry K, Labutti K, Kuo R, Ohm RA, Bhattacharya SS, Shirouzu T, Yoshinaga Y, Martin FM, Grigoriev IV, Hibbett DS. Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities. Mol Biol Evol 2015; 33:959-70. [DOI: 10.1093/molbev/msv337] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Xie N, Chapeland-Leclerc F, Silar P, Ruprich-Robert G. Systematic gene deletions evidences that laccases are involved in several stages of wood degradation in the filamentous fungusPodospora anserina. Environ Microbiol 2013; 16:141-61. [DOI: 10.1111/1462-2920.12253] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/22/2013] [Accepted: 08/11/2013] [Indexed: 02/03/2023]
Affiliation(s)
- Ning Xie
- Univ Paris Diderot, Sorbonne Paris Cité; Institut des Energies de Demain (IED); 75205 Paris France
- Univ Paris Sud; Institut de Génétique et Microbiologie; UMR8621 91405 Orsay France
| | - Florence Chapeland-Leclerc
- Univ Paris Sud; Institut de Génétique et Microbiologie; UMR8621 91405 Orsay France
- Univ Paris Descartes; Sorbonne Paris Cité; Institut des Energies de Demain (IED); 75205 Paris France
| | - Philippe Silar
- Univ Paris Diderot, Sorbonne Paris Cité; Institut des Energies de Demain (IED); 75205 Paris France
- Univ Paris Sud; Institut de Génétique et Microbiologie; UMR8621 91405 Orsay France
| | - Gwenaël Ruprich-Robert
- Univ Paris Sud; Institut de Génétique et Microbiologie; UMR8621 91405 Orsay France
- Univ Paris Descartes; Sorbonne Paris Cité; Institut des Energies de Demain (IED); 75205 Paris France
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Structural and phylogenetic analysis of laccases from Trichoderma: a bioinformatic approach. PLoS One 2013; 8:e55295. [PMID: 23383142 PMCID: PMC3561346 DOI: 10.1371/journal.pone.0055295] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 12/20/2012] [Indexed: 11/19/2022] Open
Abstract
The genus Trichoderma includes species of great biotechnological value, both for their mycoparasitic activities and for their ability to produce extracellular hydrolytic enzymes. Although activity of extracellular laccase has previously been reported in Trichoderma spp., the possible number of isoenzymes is still unknown, as are the structural and functional characteristics of both the genes and the putative proteins. In this study, the system of laccases sensu stricto in the Trichoderma species, the genomes of which are publicly available, were analyzed using bioinformatic tools. The intron/exon structure of the genes and the identification of specific motifs in the sequence of amino acids of the proteins generated in silico allow for clear differentiation between extracellular and intracellular enzymes. Phylogenetic analysis suggests that the common ancestor of the genus possessed a functional gene for each one of these enzymes, which is a characteristic preserved in T. atroviride and T. virens. This analysis also reveals that T. harzianum and T. reesei only retained the intracellular activity, whereas T. asperellum added an extracellular isoenzyme acquired through horizontal gene transfer during the mycoparasitic process. The evolutionary analysis shows that in general, extracellular laccases are subjected to purifying selection, and intracellular laccases show neutral evolution. The data provided by the present study will enable the generation of experimental approximations to better understand the physiological role of laccases in the genus Trichoderma and to increase their biotechnological potential.
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Santos CS, Pinheiro M, Silva AI, Egas C, Vasconcelos MW. Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening. BMC Genomics 2012; 13:599. [PMID: 23134679 PMCID: PMC3542250 DOI: 10.1186/1471-2164-13-599] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/30/2012] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Pine wilt disease (PWD), caused by the pinewood nematode (PWN; Bursaphelenchus xylophilus), damages and kills pine trees and is causing serious economic damage worldwide. Although the ecological mechanism of infestation is well described, the plant's molecular response to the pathogen is not well known. This is due mainly to the lack of genomic information and the complexity of the disease. High throughput sequencing is now an efficient approach for detecting the expression of genes in non-model organisms, thus providing valuable information in spite of the lack of the genome sequence. In an attempt to unravel genes potentially involved in the pine defense against the pathogen, we hereby report the high throughput comparative sequence analysis of infested and non-infested stems of Pinus pinaster (very susceptible to PWN) and Pinus pinea (less susceptible to PWN). RESULTS Four cDNA libraries from infested and non-infested stems of P. pinaster and P. pinea were sequenced in a full 454 GS FLX run, producing a total of 2,083,698 reads. The putative amino acid sequences encoded by the assembled transcripts were annotated according to Gene Ontology, to assign Pinus contigs into Biological Processes, Cellular Components and Molecular Functions categories. Most of the annotated transcripts corresponded to Picea genes-25.4-39.7%, whereas a smaller percentage, matched Pinus genes, 1.8-12.8%, probably a consequence of more public genomic information available for Picea than for Pinus. The comparative transcriptome analysis showed that when P. pinaster was infested with PWN, the genes malate dehydrogenase, ABA, water deficit stress related genes and PAR1 were highly expressed, while in PWN-infested P. pinea, the highly expressed genes were ricin B-related lectin, and genes belonging to the SNARE and high mobility group families. Quantitative PCR experiments confirmed the differential gene expression between the two pine species. CONCLUSIONS Defense-related genes triggered by nematode infestation were detected in both P. pinaster and P. pinea transcriptomes utilizing 454 pyrosequencing technology. P. pinaster showed higher abundance of genes related to transcriptional regulation, terpenoid secondary metabolism (including some with nematicidal activity) and pathogen attack. P. pinea showed higher abundance of genes related to oxidative stress and higher levels of expression in general of stress responsive genes. This study provides essential information about the molecular defense mechanisms utilized by P. pinaster and P. pinea against PWN infestation and contributes to a better understanding of PWD.
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Affiliation(s)
- Carla S Santos
- CBQF – Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Centro Regional do Porto da Universidade Católica Portuguesa, Rua Dr. António Bernardino Almeida, Porto, 4200-072, Portugal
| | - Miguel Pinheiro
- Bioinformatics Unit, Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 03, Cantanhede, 3060-197, Portugal
| | - Ana I Silva
- CBQF – Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Centro Regional do Porto da Universidade Católica Portuguesa, Rua Dr. António Bernardino Almeida, Porto, 4200-072, Portugal
| | - Conceição Egas
- Advanced Services Unit, Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 03, Cantanhede, 3060-197, Portugal
| | - Marta W Vasconcelos
- CBQF – Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Centro Regional do Porto da Universidade Católica Portuguesa, Rua Dr. António Bernardino Almeida, Porto, 4200-072, Portugal
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